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libSBML C++ API
5.18.0
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libSBML C++ API
5.18.0
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SBML Level 3 introduced a modular architecture, in which SBML Level 3 Core is usable in its own right (much like SBML Levels 1 and 2 before it), and optional SBML Level 3 Packages add features to this Core. To support this architecture, libSBML is itself divided into a core libSBML and optional extensions.
Core libSBML corresponds to the features of SBML Levels 1 to 3 Core; they are always available, and require applications to understand only the SBML core specifications. The classes listed on the rest of this page constitute libSBML's implementation of SBML Levels 1–3, without any SBML Level 3 packages.
By contrast, the libSBML extensions are plug-ins that each implement support for a given SBML Level 3 package. Separate pages of this API manual describe the libSBML extensions for those SBML Level 3 packages that are supported at this time. They are grouped under the section titled Level 3 Extensions. The stable releases of libSBML only include extensions for officially-released package specifications; additional, experimental extensions may be available for other Level 3 packages that may not yet have been finalized by the SBML community. You can find copies of these experimental extensions at the download site for libSBML on SourceForge.net.
Each type of component in a plain SBML model (i.e., one that does not use any SBML packages) is described using a specific type of SBML data object that organizes the relevant information. The top level of an SBML model definition consists of lists of these components, with every list being optional. The next table enumerates the lists and objects defined by core SBML; also shown are the SBML Level+Version combinations for which they are valid.
| Level & Version | LibSBML container object | LibSBML data object(s) |
|---|---|---|
| Level 2 Version 1 and higher | ListOfFunctionDefinitions | FunctionDefinition |
| Level 2 Version 1 and higher | ListOfUnitDefinitions | UnitDefinition |
| Level 2 Versions 2–5 | ListOfCompartmentTypes | CompartmentType |
| Level 1 and higher | ListOfCompartments | Compartment |
| Level 2 Versions 2–5 | ListOfSpeciesTypes | SpeciesType |
| Level 1 and higher | ListOfSpecies | Species |
| Level 1 and higher | ListOfParameters | Parameter |
| Level 2 Version and higher | ListOfInitialAssignments | InitialAssignment |
| Level 1 and higher | ListOfRules | AssignmentRule, AlgebraicRule, RateRule |
| Level 2 Version and higher | ListOfConstraints | Constraint |
| Level 1 and higher | ListOfReactions | Reaction |
| Level 2 Version 1 and higher | ListOfEvents | Event |
The list of classes below constitutes the public API of core libSBML. The list includes classes that are not defined in any SBML specification; these utility classes are provided by libSBML to implement various kinds of functionality useful in the context of working with SBML content. More...
Classes | |
| class | AlgebraicRule |
| An SBML algebraic rule representing 0 = f(W). More... | |
| class | AssignmentRule |
| An SBML assignment rule representing x = f(Y). More... | |
| class | ASTNode |
| Abstract Syntax Tree (AST) representation of a mathematical expression. More... | |
| class | Compartment |
| An SBML compartment, where species are located. More... | |
| class | CompartmentType |
| A compartment type in SBML Level 2. More... | |
| class | Constraint |
| An SBML constraint, for stating validity assumptions. More... | |
| class | ConversionOption |
| A single configuration setting for an SBML converter. More... | |
| class | ConversionProperties |
| Set of configuration option values for a converter. More... | |
| class | CVTerm |
| A MIRIAM-compliant controlled vocabulary term. More... | |
| class | Date |
| A MIRIAM-compliant date representation. More... | |
| class | DefinitionURLRegistry |
| Registry of all libSBML SBML DefinitionURLs. More... | |
| class | Delay |
| A delay on the time of execution of an SBML event. More... | |
| class | ElementFilter |
| Base class for filter functions. More... | |
| class | Event |
| A discontinuous SBML event. More... | |
| class | EventAssignment |
| An assignment to a variable by an SBML event. More... | |
| struct | FormulaTokenizer_t |
| used to track the state of tokenizing a string. More... | |
| class | FunctionDefinition |
| A user-defined function in an SBML model. More... | |
| class | InitialAssignment |
| An SBML initial assignment, evaluated once only. More... | |
| class | KineticLaw |
| The rate expression for an SBML reaction. More... | |
| class | L3ParserSettings |
| Controls the behavior of the Level 3 formula parser. More... | |
| class | List |
| Simple, plain, generic lists. More... | |
| class | ListOf |
| Parent class for libSBML's "ListOfXYZ" classes. More... | |
| class | ListOfCompartments |
| A list of Compartment objects. More... | |
| class | ListOfCompartmentTypes |
| A list of CompartmentType objects. More... | |
| class | ListOfConstraints |
| A list of Constraint objects. More... | |
| class | ListOfEventAssignments |
| A list of EventAssignment objects. More... | |
| class | ListOfEvents |
| A list of Event objects. More... | |
| class | ListOfFunctionDefinitions |
| A list of FunctionDefinition objects. More... | |
| class | ListOfInitialAssignments |
| A list of InitialAssignment objects. More... | |
| class | ListOfLocalParameters |
| A list of LocalParameter objects. More... | |
| class | ListOfParameters |
| A list of Parameter objects. More... | |
| class | ListOfReactions |
| A list of Reaction objects. More... | |
| class | ListOfRules |
| A list of Rule objects. More... | |
| class | ListOfSpecies |
| A list of Species objects. More... | |
| class | ListOfSpeciesReferences |
| A list of SpeciesReference objects. More... | |
| class | ListOfSpeciesTypes |
| A list of SpeciesType objects. More... | |
| class | ListOfUnitDefinitions |
| A list of UnitDefinition objects. More... | |
| class | ListOfUnits |
| A list of Unit objects. More... | |
| class | LocalParameter |
| A parameter inside an SBML reaction definition. More... | |
| class | Model |
| An SBML model. More... | |
| class | ModelCreator |
| MIRIAM-compliant data about a model's creator. More... | |
| class | ModelHistory |
| MIRIAM-compliant data about a model's history. More... | |
| class | ModifierSpeciesReference |
| A reference to an SBML modifier species. More... | |
| class | Parameter |
| An SBML parameter: a named symbol with a value. More... | |
| class | Priority |
| The priority of execution of an SBML event. More... | |
| class | RateRule |
| An SBML rate rule representing dx/dt = f(Y). More... | |
| class | RDFAnnotationParser |
| MIRIAM-compliant RDF annotation reader/writer. More... | |
| class | Reaction |
| An SBML reaction between species in an SBML model. More... | |
| class | RenderLayoutConverter |
| Converts an SBML document with Layout and Render information between the Level 3 package version and the Level 2 annotation version. More... | |
| class | Rule |
| Parent class for SBML rules in libSBML. More... | |
| class | SBase |
| SBML's SBase class, base class of most SBML objects. More... | |
| class | SBaseExtensionPoint |
| Base class for extending SBML components More... | |
| class | SBasePlugin |
| Base class for extending SBML objects in packages. More... | |
| class | SBasePluginCreator< SBasePluginType, SBMLExtensionType > |
| Template for SBasePlugin factory objects. More... | |
| class | SBasePluginCreatorBase |
| Base class of SBasePluginCreator. More... | |
| class | SBMLConstructorException |
| Exceptions thrown by some libSBML constructors. More... | |
| class | SBMLConverter |
| Base class for SBML converters. More... | |
| class | SBMLConverterRegister< SBMLConversionType > |
| Template for SBML converter registry registrations. More... | |
| class | SBMLConverterRegistry |
| Registry of all libSBML SBML converters. More... | |
| class | SBMLDocument |
| Overall SBML container object. More... | |
| class | SBMLDocumentPlugin |
| Base class for extending SBMLDocument in packages. More... | |
| class | SBMLDocumentPluginNotRequired |
| Base class for non-required Level 3 packages plug-ins. More... | |
| class | SBMLError |
| An error, warning or other diagnostic. More... | |
| class | SBMLErrorLog |
| Log of diagnostics reported during processing. More... | |
| class | SBMLExtension |
| Base class for SBML Level 3 package plug-ins. More... | |
| class | SBMLExtensionException |
| Exception used by package extensions More... | |
| class | SBMLExtensionNamespaces< SBMLExtensionType > |
| Set of SBML Level + Version + namespace triples. More... | |
| class | SBMLExtensionRegister< SBMLExtensionType > |
| Template class for extension package registration More... | |
| class | SBMLExtensionRegistry |
| Registry where package extensions are registered. More... | |
| class | SBMLFunctionDefinitionConverter |
| Converter to expand user-defined functions in-line. More... | |
| class | SBMLIdConverter |
| Converter for replacing object identifiers. More... | |
| class | SBMLInferUnitsConverter |
| Converter for inferring and setting parameter units. More... | |
| class | SBMLInitialAssignmentConverter |
| Converter that removes SBML initial assignments. More... | |
| class | SBMLInternalValidator |
| Basic SBML consistency checks and other validations. More... | |
| class | SBMLLevel1Version1Converter |
| Whole-document SBML Level/Version converter. More... | |
| class | SBMLLevelVersionConverter |
| Whole-document SBML Level/Version converter. More... | |
| class | SBMLLocalParameterConverter |
| Converter to turn local parameters into global ones. More... | |
| class | SBMLNamespaces |
| Set of SBML Level + Version + namespace triples. More... | |
| class | SBMLRateOfConverter |
| Converter to inteerchange csymbol 'rateOf' with FunctionDefinition. More... | |
| class | SBMLReactionConverter |
| Converter to replace reactions with SBML rate rules. More... | |
| class | SBMLReader |
| File and text-string SBML reader. More... | |
| class | SBMLRuleConverter |
| Converter that sorts SBML rules and assignments. More... | |
| class | SBMLStripPackageConverter |
| Converter that removes SBML Level 3 packages. More... | |
| class | SBMLUnitsConverter |
| Converts a model's existing units to SI units. More... | |
| class | SBMLValidator |
| Base class for SBML validators. More... | |
| class | SBMLVisitor |
| Support class for operations on SBML objects. More... | |
| class | SBMLWriter |
| File and text-string SBML writer. More... | |
| class | SBO |
| Facilities for using the Systems Biology Ontology. More... | |
| class | SimpleSpeciesReference |
| Abstract class for references to species in reactions. More... | |
| class | Species |
| An SBML species – a pool of entities. More... | |
| class | SpeciesReference |
| A reference to an SBML species in a reaction. More... | |
| class | SpeciesType |
| A species type in SBML Level 2. More... | |
| class | StoichiometryMath |
| Stochiometry expressions in SBML Level 2 reactions. More... | |
| class | SyntaxChecker |
| Methods for checking the validity of SBML identifiers. More... | |
| struct | Token_t |
| Structure used to store a token returned by FormulaTokenizer_nextToken(). More... | |
| class | Trigger |
| The trigger expression for an SBML event. More... | |
| class | Unit |
| A single unit referenced in an SBML unit definition. More... | |
| class | UnitDefinition |
| A definition of a unit used in an SBML model. More... | |
| class | Validator |
| Entry point for SBML validation rules in libSBML. More... | |
| class | VConstraint |
| Helper class for SBML validators. More... | |
| class | XMLAttributes |
| A list of attributes on an XML element. More... | |
| class | XMLConstructorException |
| Exceptions thrown by some libSBML constructors. More... | |
| class | XMLError |
| XML-level errors, warnings and other diagnostics. More... | |
| class | XMLErrorLog |
| Log of diagnostics reported during XML processing. More... | |
| class | XMLInputStream |
| An interface to an XML input stream. More... | |
| class | XMLLogOverride |
| Facility for temporarily overriding error severities. More... | |
| class | XMLNamespaces |
| An XML Namespace. More... | |
| class | XMLNode |
| A node in libSBML's XML document tree. More... | |
| class | XMLOutputStream |
| Interface to an XML output stream. More... | |
| class | XMLToken |
| A token in an XML stream. More... | |
| class | XMLTriple |
| A qualified XML name. More... | |
SBML Level 3 introduced a modular architecture, in which SBML Level 3 Core is usable in its own right (much like SBML Levels 1 and 2 before it), and optional SBML Level 3 Packages add features to this Core. To support this architecture, libSBML is itself divided into a core libSBML and optional extensions.
Core libSBML corresponds to the features of SBML Levels 1 to 3 Core; they are always available, and require applications to understand only the SBML core specifications. The classes listed on the rest of this page constitute libSBML's implementation of SBML Levels 1–3, without any SBML Level 3 packages.
By contrast, the libSBML extensions are plug-ins that each implement support for a given SBML Level 3 package. Separate pages of this API manual describe the libSBML extensions for those SBML Level 3 packages that are supported at this time. They are grouped under the section titled Level 3 Extensions. The stable releases of libSBML only include extensions for officially-released package specifications; additional, experimental extensions may be available for other Level 3 packages that may not yet have been finalized by the SBML community. You can find copies of these experimental extensions at the download site for libSBML on SourceForge.net.
Each type of component in a plain SBML model (i.e., one that does not use any SBML packages) is described using a specific type of SBML data object that organizes the relevant information. The top level of an SBML model definition consists of lists of these components, with every list being optional. The next table enumerates the lists and objects defined by core SBML; also shown are the SBML Level+Version combinations for which they are valid.
| Level & Version | LibSBML container object | LibSBML data object(s) |
|---|---|---|
| Level 2 Version 1 and higher | ListOfFunctionDefinitions | FunctionDefinition |
| Level 2 Version 1 and higher | ListOfUnitDefinitions | UnitDefinition |
| Level 2 Versions 2–5 | ListOfCompartmentTypes | CompartmentType |
| Level 1 and higher | ListOfCompartments | Compartment |
| Level 2 Versions 2–5 | ListOfSpeciesTypes | SpeciesType |
| Level 1 and higher | ListOfSpecies | Species |
| Level 1 and higher | ListOfParameters | Parameter |
| Level 2 Version and higher | ListOfInitialAssignments | InitialAssignment |
| Level 1 and higher | ListOfRules | AssignmentRule, AlgebraicRule, RateRule |
| Level 2 Version and higher | ListOfConstraints | Constraint |
| Level 1 and higher | ListOfReactions | Reaction |
| Level 2 Version 1 and higher | ListOfEvents | Event |
The list of classes below constitutes the public API of core libSBML. The list includes classes that are not defined in any SBML specification; these utility classes are provided by libSBML to implement various kinds of functionality useful in the context of working with SBML content.
